About the root you are right, and I want to add that it's better to use sudo.
You can limit yourself as a superuser(can only change several environment variables and more-Not acces to all the system).

emerge -Du system will update your system development tools so you and will probablyl break some packages.
If you still want to update your system and gcc...you should type emerge -e world...

emerge -Du world is perfectly fine when you just want to update your programs...
It has nothing to do with emerge -Du system, except the emerge -Du._________________Linux, if it's broken fix it!
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Hmm... I kinda disagree with this one. I understand that it really makes no sense to work with gentoo unless one uses portage, but in some cases, the portage packages are more hassle than installing something on your own.

Here's an example:

I use texlive rather than tetex. Since I'm on ppc, I need to compile all the tetex binaries because texlive doesn't supply them for linux-ppc. It is generally a Big Hassle to have two TeX installations, so I do it myself rather than use portage. (And even on x86 you probably wouldn't want to use portage if you were going to use texlive.) With texlive, I get TeX/LaTeX stuff that portage masks. (why? they're just TeX/LaTeX packages) In general, texlive is a lot easier to deal with than the ebuilds.

There are also times when you need something immediately and the ebuild is broken or behind the curve. I guess the gentoo thing to do is fix it or update the ebuild, but that doesn't always happen.

I agree with e-ipi: some programs aren't in portage. Instead of writing an ebuild for them, you can just install them in /usr/share/local, where they belong.
All programs not installed by some package manager go in /usr/share/local, that's why there is such a directory...

My all-time favorite: always do rc-update del xdm, before fiddling with an xorg.conf. If your X crashes or boots without proper keyboard input, you'll have to search another pc to be able to reboot using ssh.

my all time favorite: never ever type shutdown -h / init 0 into a shell unless you have physical access to the box...

a good habit is to open a new xterm before su-ing and shutdown -h-ing.... if you use an open one, you might use one that is ssh-ed into another box. woops!_________________my website, built in HAppS: http://dbpatterson.com
an art (oil painting) website I built a pure python backend for: http://www.lydiajohnston.com

happened to me twice
i was in need to reboot the laptop to do some windoze stuff so i typed reboot and ctrl-d several times to logout and close aterm. after a minute it was a bit suspicious that nothing happened. of course, i typed it to a terminal ssh-ed to my server. by mistakes we learn...

and my favorite one(related to remote administration) - never type iptables -F before ensuring that default input policy is ACCEPT

why it isn't good to emerge several packages in different terminal?
I always do emerge in different ttys, but they are different programs always.

Yeah, portage has pretty good file locking. I almost always run emerge -f package along side the normal emerge (so the packages will be downloading while the others compile)._________________"Someday, he thought, it'll be mandatory that we all sell the McDonald's hamburger as well as buy it; we'll sell it back and forth to each other forever from our living rooms. That way we won't even have to go outside." - A Scanner Darkly By PK Dick

time() ?
... Do you mean, start them at precisely the same moment in time? It's a little hard to do anyway.
I usually do several emerges together. I'd go insane otherwise._________________Votre moment detenteWhat is the nature of conflict?

Indeed, though I seem to remember at one time they wanted to do away with that reasoning that "modern package managers remove the need for the separate hierarchy"?_________________Please put [SOLVED] in your topic if you are a moron.

emerge -C python_________________the table is made from wood. forget what you learnt, the table is made from carbon. forget what you learnt, the table is made from protons. forget what you learnt, the table is made from quarks. forget what you learnt, the table is good for shagging on